EPYC

epiphycan, the group of Small leucine rich repeat proteoglycans

Basic information

Region (hg38): 12:90963682-91005026

Previous symbols: [ "DSPG3" ]

Links

ENSG00000083782 ∙ NCBI:1833 ∙ OMIM:601657 ∙ HGNC:3053 ∙ Uniprot:Q99645 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EPYC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EPYC gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			32			32
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region					1	1
non coding						0
Total	0	0	32	2	0

Variants in EPYC

This is a list of pathogenic ClinVar variants found in the EPYC region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-90964165-G-T		not specified	Uncertain significance (May 17, 2023)
12-90964182-G-A		not specified	Uncertain significance (Mar 14, 2023)
12-90964212-T-C		not specified	Uncertain significance (Nov 17, 2022)
12-90964223-A-G		not specified	Uncertain significance (Sep 14, 2022)
12-90964245-T-C		not specified	Uncertain significance (Mar 28, 2024)
12-90964262-C-T		not specified	Uncertain significance (Apr 12, 2022)
12-90964273-C-G		not specified	Uncertain significance (Nov 22, 2021)
12-90964303-G-C		not specified	Uncertain significance (Jul 14, 2023)
12-90970093-T-G		not specified	Uncertain significance (Oct 04, 2022)
12-90970136-T-A		not specified	Uncertain significance (Jan 05, 2022)
12-90970136-T-C		not specified	Uncertain significance (Jul 13, 2022)
12-90971799-C-G			Likely benign (Jan 23, 2018)
12-90971846-C-T		not specified	Uncertain significance (Oct 29, 2021)
12-90971850-T-C		not specified	Uncertain significance (Jun 07, 2024)
12-90971906-C-T		not specified	Uncertain significance (Jan 02, 2024)
12-90971907-G-A		not specified	Uncertain significance (Feb 22, 2023)
12-90971921-C-T		not specified	Uncertain significance (Apr 17, 2024)
12-90971940-G-A			Likely benign (Dec 31, 2019)
12-90972896-G-A		not specified	Uncertain significance (Jun 24, 2022)
12-90972911-G-A		not specified	Uncertain significance (Nov 09, 2021)
12-90972935-T-C		not specified	Uncertain significance (Dec 05, 2022)
12-90972939-C-T		not specified	Uncertain significance (Dec 11, 2023)
12-90972959-C-T		not specified	Uncertain significance (Sep 14, 2022)
12-90972979-G-C		not specified	Uncertain significance (Aug 13, 2021)
12-90978092-A-T		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EPYC	protein_coding	protein_coding	ENST00000261172	6	41348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.75e-7	0.443	125428	2	314	125744	0.00126

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.264	179	169	1.06	0.00000833	2110
Missense in Polyphen		38	39.961	0.95093		513
Synonymous	0.359	61	64.7	0.943	0.00000323	632
Loss of Function	0.701	11	13.8	0.796	8.83e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.00187	0.00169
Finnish	0.00	0.00
European (Non-Finnish)	0.000416	0.000396
Middle Eastern	0.00187	0.00169
South Asian	0.00769	0.00754
Other	0.000673	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a role in bone formation and also in establishing the ordered structure of cartilage through matrix organization.

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.621
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.1

Haploinsufficiency Scores

• pHI: 0.0721
• hipred: N
• hipred_score: 0.350

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.179

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Epyc
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; immune system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: female pregnancy
• Cellular component: extracellular region
• Molecular function: glycosaminoglycan binding